Abstract

Recombination plays an important role in creating genetic diversity within species, and inferring past recombination events is central to many problems in genetics. Given a set M of sampled sequences, finding an evolutionary history for M with the minimum number of recombination events is a computationally very challenging problem. In this paper, we present a novel branch and bound algorithm for tackling that problem. Our method is shown to be far more efficient than the only preexisting exact method, described in [1]. Our software implementing the algorithm discussed in this paper is publicly available.

Hudson, R.R., Kaplan, N.L.: Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111, 147–164 (1985)

3.

Myers, S.R., Griffiths, R.C.: Bounds on the minimum number of recombination events in a sample history. Genetics 163, 375–394 (2003)

4.

Gusfield, D., Hickerson, D.: A new lower bound on the number of needed recombination nodes in both unrooted and rooted phylogenetic networks. Technical Report UCD-ECS-06, University of California, Davis (2004)

5.

Song, Y.S., Hein, J.: On the minimum number of recombination events in the evolutionary history of DNA sequences. Journal of Mathematical Biology 48, 160–186 (2004)MATHCrossRefMathSciNet